Markov Chains in JS — Part 1

I'm in the process of writing a new post or two on working with Markov Chains in javascrtipt. I created the javascript files already and I've decided to post them below for now. I'll write up more about it and hopefully use the code for something interesting in a future post. See below for the javascript Markov Chain Simulator! See the code here.

Amino Acid Interactions

I couldn't find a nice table of amino acid interaction energies, so I created one from crystallography data of thousands of protein. Here are the results and an explanation of how I did it. There is also a black and white version in the article which could be nice for printing. I don't know, I printed a pdf but blogger won't host pdfs for me.

SIS Stochastic Model: Distributions and Proportional Probability

In this post, I'll describe how to go from the SIS model to a zombie model. The results are a stochastic simulation, shown below. There are few items on the model TODO list: add spatial variables and zombie deaths/kills.

SIS Stochastic Model: On the Road to Zombies

Epidemiology has many interesting models for describing disease outbreaks. A large class of these models, the only ones with which I'm familiar in fact, are known as compartment models. One of the most amusing extensions of these models is incorporating a zombie compartment, or population. A researcher named Robert J. Smith? has developed some deterministic models for describing these zombie models. Not totally sure why he publishes with a question mark; I assume to differentiate his citation counts from all the other Robert Smiths. Anyway, his publications can be found here. It's interesting stuff, but I think I can do it with a stochastic version. In Part 1 of an unknown number, I'll introduce the SIS model and some matrix techniques for working with it. In Part 2, to be written, I'll move to Markov probability distributions instead of matrices and introduce zombies.